| Modern wheat cultivars consist of two species,the durum wheat(Triticum turgidum ssp.durum,2n=4x=28,AABB)and common wheat(T.aestivum ssp.aestivum,2n=6x=42,AABBDD),among which durum wheat contributes to 5%of world wheat production and 10%of world wheat cultivation area.However,durum wheat has high protein and carotene content,which makes it the exclusive raw material for pasta and other semolina foods.Therefore,durum wheat has 20%higher market price than common wheat and has irreplaceable agricultural and economic value.Compared with common wheat,durum wheat is mainly cultivated in arid or semi-arid areas,which makes durum wheat more adaptable to drought stress.There are wide differences in genetic diversity and many phenotypic characters between durum wheat and common wheat,and therefore,durum wheat and common wheat are the main gene pools for each other in breeding.Durum wheat and common wheat(the AB genomes)may evolved from different subgroups of domesticated emmer wheat(T.turgidum ssp.dicoccum,AABB,2n=4x=28),which may be a main source for their difference in genetic diversity,but so far,the genetic relationship between the three species has poorly understood.Currently,by using linkage analysis or association analysis,many studies on QTL mapping have been carried out in wheat agronomic traits and drought resistance,but the researches most focused on common wheat rather than durum wheat.In this study,we carried out a systematic study on the genetic diversity of a core germplasm of national small grain collection(NSGC)by genotype data from wheat 9K SNP array and phenotypes from 18 main agronomic traits and drought resistance(wilting index).The main results are as follows:1.The results showed that durum wheat has abundant genetic and phenotypic variation.The 18 agronomic traits investigated had high heritability(H2=60%?92%),among which plant height,heading time,flag leaf length,flag leaf angle,spike length and spikelet number were selected in the previous breeding process.4,369 SNP markers with high polymorphism(MAF>0.05)were identified by wheat 9K SNP array,covering all 14 chromosomes with an average density of 2.6 Mb.The degree of linkage disequilibrium decreased rapidly with physical distance greater than 5 Mb,and generally,it was estimated that at least 26 Mb was needed for r2 to decrease to 0.1.2.It is found that the population of durum wheat has a complex hierarchical structure,which is embodied in a high degree of genetic correlation between subpopulations or materials.The peak value of IBS distribution was 0.6,which indicated that there was a high level of relationship between different materials.Through the calculation of genetic composition of each material by STRUCTURE software,it was found that durum wheat population could be divided into two or four subgroups,among which a large number of materials showed mixed genetic composition:whether divided into two or four subgroups,29%and 47%of material Q value(the proportion of the largest genetic composition)were less than 0.7,and breeding status or geographic distribution were also found to less correlated with the genetic division of subgroups.3.The genetic diversity of modern cultivated wheat(durum and common wheat)and domesticated emmer wheat were compared.It was found that there was obvious bottleneck effect in the process of domestication and breeding from ancestors to landraces,then to improved varieties,revealed by the decrease of genetic diversity.The three wheat species showed significant genetic differentiation,among which durum wheat and common wheat showed the highest level of genetic differentiation.Furthermore,the genetic composition of the three materials was calculated by STRUCTURE software,which showed that the genetic relationship of the three materials was related to their evolutionary process:domesticated emmer wheat was clearly divided into two subgroups,the southern and northern subgroups which were genetically and geographically different,most of the genetic composition of durum wheat was similar to that of the southern subgroups of domesticated emmer wheat,and all the common wheat materials were similar to that of the northern subgroups of domesticated emmer wheat,indicating that durum wheat and common wheat may originate from different domesticated emmer wheat subgroups,and the population differentiation of domesticated emmer wheat may be an important reason for the genetic diversity difference between durum wheat and common wheat.4.Association study identified 121 SNP markers(belonging to 73 genetic loci)for 17 agronomic traits.For different traits,the number of related loci varies from 1 to 14.A single locus can account for 2%?6%of the phenotypic variation,and all loci can account for 6%?43%of the phenotypic variation,which mainly depends on the number of related loci detected.Combined marker-assisted breeding(only considering the related loci)and genomic selection(using all 4369 polymorphic markers),it was found that for all traits,the prediction ability of genomic selection on the phenotypic value was higher than that of marker-assisted breeding,which indicated that the association analysis did not detect the minor-effect QTL,and that most of the agronomic traits concerned in this study were typical quantitative traits which controlled by both the major-effect and minor-effect QTL.Among 121 related markers and 73 related loci,16 and 15 were significantly associated with multiple traits,respectively,which indicated that pleiotropy or genetic linkage existed widely under QTL of agronomic traits of durum wheat.Using two F2:3 populations,we further verified the three pleiotropic yield-related sites by linkage analysis.The results showed that results from linkage analysis and association study were completely consistent,indicating the reliability of the association study.5.Association study showed that 19 SNP markers(belonging to 9 genetic loci)were significantly associated with drought resistance(wilting index).Locus.4B.1 has been widely reported to be related to a variety of drought resistance and salt tolerance indexes in durum wheat and common wheat before.In addition,locus.4B.1 was significantly related to plant height at the same time,which may be due to the fact that locus.4B.1 was located in the downstream of Rht-B1 gene,and they had a certain degree of genetic linkage with Rht-B1.Haplotype analysis showed that there were 9 haplotypes(hap 1-9)in locus.4B.1.The haplotype distribution was consistent with the evolutionary history of durum wheat,common wheat and domesticated emmer wheat.In durum wheat population,only two haplotypes hapl and hap2 with low frequency(12%in total)showed drought resistance,and they were related to the relatively low plant height.These two haplotypes were selected in the breeding process,but they were not fixed yet,so they have potential application in durum improvement.6.Through integrating QTL positions reported previously,we reduced the physical position of locus.4B.1 to a 16 Mb interval including 177 annotation genes.Combined with information of gene annotation,expression pattern and sequence variation,we found that three tandemly repeated genes TaWD40.4B.1?3 with seven WD40 domains may be candidate genes for the site,and the mutation CDS.1274.G>A on TaWD40.4B.2 leading to premature termination may be the functional variation of this site.The statistical analysis showed that the drought resistance of the lines carrying CDS.1274.G was significantly higher than that of the lines carrying CDS.1274.A.We further analyzed the drought resistance phenotype of durum wheat EMS mutant of TaWD40.4B.1?3,and found that the three genes were conserved in drought resistance function,and different domains had different effects on drought resistance. |
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